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It should download a hex file ".hex". Something like "MarlinUltimaker-UMO-250000.hex".

Then in ie, or firefox or chrome you right click it and do "show in folder" or similar.

Next you connect your computer to your printer through USB and run Cura and do Machine "install custom firmware..." and choose the hex file. It's pretty safe, the bootloader in the arduino is protected so even if you load bad firmware you can always load proper firmware later.

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Now the funny thing is that when you write a plugin, Cura add a 'help' button that redirects on the old ultimaker wiki, and I discover that way that somebody already made a plugin with the same name doing the same thing

If you have GT2 pulleys, there is an option to set the right X/Y steps/u in the firmware(This is not strictly necessary as you can edit and save this setting in nvram from the controller, but I like it this way )